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Summary

BioMart::Formatter::FASTA

Package variables

Inherit

BioMart::FormatterI

Synopsis

The FASTA Formatter returns whitespace separated tabular data
for a BioMart query's ResultTable

Description

When given a BioMart::ResultTable containing the results of
a BioMart::Query the FASTA Formatter will return tabular output
with one line for each row of data in the ResultTable and single spaces
separating the individual entries in each row. The getDisplayNames
and getFooterText can be used to return appropiately formatted
headers and footers respectively

Methods

Methods description

None available.

Methods code

sub _new {

    my ($self) = @_;

    $self->SUPER::_new();

}

sub getDisplayNames {

    my $self = shift;

    return '';

}

sub isSpecial {

    return 1;
}

1;

}

sub nextRow {

    my $self = shift;

    my $rtable = $self->get('result_table');
    my $row = $rtable->nextRow;
    if (!$row){
        return;
    }
    my $array_length = @{$row};
    map { $_ = '' unless defined ($_); } @$row; # get rid of unitialized-value warning message
    my $header_atts = join "|",@{$row}[1..$array_length-1];
    
    #chop $header_atts;
    
    my $seq = ${$row}[0];
    ### SPECIAL LOGIC FOR SNP SEQUENCES, to make them agree with FASTA FORMAT
    ### THE * would suggest the split between two sequnce snp sequences
    ### The allele would go into header, which comes from genomic sequence
    ### in tags separating two snp sequences and that gets replaced by _,
    ### this tag look like %allele%. eg. %A/T%. I am using this assumption
    ### of % sign as TO DATE i have never seen a residue string containing
    ### % sign, 
    ### for those how want to post process them in a different way, may use _
    ### as a splitting point
    if ($seq =~ m/\%(.*)\%/)
    {
		$header_atts .= "|$1";
		## also substiture with *
		$seq =~ s/\%.*\%/\_/;
    }
    
    ########################################################################
    $seq =~ s/(\w{60})/$1\n/g;
    return ">" . $header_atts . "\n"
	       . $seq ."\n";

}

sub processQuery {

    my ($self, $query) = @_;

    $self->set('original_attributes',[@{$query->getAllAttributes()}]) 
	if ($query->getAllAttributes());
    $self->set('query',$query);
    return $query;

}

General documentation

This module is part of the BioMart project
http://www.biomart.org
Questions can be posted to the mart-dev mailing list: mart-dev@ebi.ac.uk